I know there are conflicting reports on the cause of this bug in Gateway 3ds and how to prevent it long time ago , but it still a commen problem among many gateway users .maybe other 3ds flashcart users , such r4i gold 3ds deluxe edition and mt-card .

Many people would meet this issue: the 3ds freezing/hanging after exiting a game improperly , resulting in the save not properly being transferred to the SD card.

The root cause of this is that the 3DS hack doesn’t always properly initialize, and so it doesn’t return after exiting a game.

The only way to prevent your game savedata lost is to run it and then exit the game after it reaches the main menu. If that exit to the home menu works properly (which means it doesn’t freeze) then all future exits should work properly during that current run of the 3DS hack, meaning your saves will transfer to the SD card properly (until you re-enter Nintendo DS profile and thus re-initialize the 3DS hack).

Here is the solution for your information :If your system froze when exiting a game, don’t never ever launch the game again! (Please note: If you launch a game after the freeze, the savegame will be lost, either replaced by the save of the new game, or deleted if the new game has no save. )
Actually , your progress is not lost yet, the save is still on the flashcart.

So , What we should to do now ?
Firstly , restart the system and enter Gateway mode.

Then , remove the micro SD card (the system should warn you at that point about removing micro SD cards when the power is on; you can usually just ignore that), and then boot the game.

Thirdly ,after confirming that your save wasn’t lost in pc (connect the micro sd card to pc by using card reader ), insert the micro SD back in and exit the game by pressing the Home button and then Close.

At this point the game should close, and the save should have been safely copied to the micro SD card.